![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| crlmm-package | Genotype Calling via CRLMM Algorithm |
| ABpanel | A panel function for plotting prediction regions and log-normalized intensities |
| BafLrrSetList | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~ |
| BafLrrSetList-method | crlmm methods for class "CNSet" |
| CA | Accessors for allele-specific or total copy number |
| CA-method | crlmm methods for class "CNSet" |
| calculateRBaf | Calculate log R ratios and B allele frequencies. |
| calculateRBaf-method | Calculate log R ratios and B allele frequencies. |
| CB | Accessors for allele-specific or total copy number |
| CB-method | crlmm methods for class "CNSet" |
| celDates | Reads cel files and return an error if a file is not read |
| cnrmaAffy | quantile normalize nonpolymorphic markers |
| cnSetExample | Object of class 'CNSet' |
| cnSetExample2 | Object of class 'CNSet' |
| coerce-method | crlmm methods for class "CNSet" |
| constructAffyCNSet | Construct an object of class CNSet from Affymetrix cel files |
| constructInf | Instantiate an object of class CNSet for the Infinium platforms. |
| corr | Accessors for batch-specific summary statistics. |
| corr-method | Methods for class "AssayData" in crlmm |
| corr-method | crlmm methods for class "CNSet" |
| crlmm | Genotype oligonucleotide arrays with CRLMM |
| crlmm2 | Genotype oligonucleotide arrays with CRLMM |
| crlmmCopynumber | Locus- and allele-specific estimation of copy number |
| crlmmCopynumber2 | Locus- and allele-specific estimation of copy number |
| crlmmCopynumberLD | Locus- and allele-specific estimation of copy number |
| crlmmIllumina | Preprocessing and genotyping of Illumina Infinium II arrays. |
| genotype | Preprocessing and genotyping of Affymetrix arrays. |
| genotype.Illumina | Preprocessing and genotyping of Illumina Infinium II arrays. |
| genotype2 | Preprocessing and genotyping of Affymetrix arrays. |
| genotypeAffy | Genotype Affymetrix CEL files |
| genotypeInf | Genotyping of Illumina Infinium II arrays. |
| genotypeLD | Preprocessing and genotyping of Affymetrix arrays. |
| genotypes | The possible genotypes for an integer copy number. |
| lines-method | crlmm methods for class "CNSet" |
| mads | Accessors for batch-specific summary statistics. |
| mads-method | Methods for class "AssayData" in crlmm |
| mads-method | crlmm methods for class "CNSet" |
| medians | Accessors for batch-specific summary statistics. |
| medians-method | Methods for class "AssayData" in crlmm |
| medians-method | crlmm methods for class "CNSet" |
| Ns | Accessors for batch-specific summary statistics. |
| Ns-method | Methods for class "AssayData" in crlmm |
| Ns-method | crlmm methods for class "CNSet" |
| nuA | Accessors for allele-specific or total copy number |
| nuA-method | crlmm methods for class "CNSet" |
| nuB | Accessors for allele-specific or total copy number |
| nuB-method | crlmm methods for class "CNSet" |
| OligoSetList | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~ |
| OligoSetList-method | crlmm methods for class "CNSet" |
| phiA | Accessors for allele-specific or total copy number |
| phiA-method | crlmm methods for class "CNSet" |
| phiB | Accessors for allele-specific or total copy number |
| phiB-method | crlmm methods for class "CNSet" |
| plotSamples | Make M vs S plot for SNPs or samples. |
| plotSNPs | Make M vs S plot for SNPs or samples. |
| posteriorProbability | Calculate the posterior probability for integer copy numbers. |
| posteriorProbability-method | Calculate the posterior probability for integer copy numbers. |
| predictionRegion | Prediction regions for integer copy number |
| PredictionRegion-class | Class '"PredictionRegion"' |
| predictionRegion-method | Prediction regions for integer copy number |
| preprocessInf | Preprocessing of Illumina Infinium II arrays. |
| rawCopynumber | Accessors for allele-specific or total copy number |
| rawCopynumber-method | crlmm methods for class "CNSet" |
| readGenCallOutput | Read X and Y intensities from GenCall output |
| readIdatFiles | Reads Idat Files from Infinium II Illumina BeadChips |
| readIdatFiles2 | Reads Idat Files from Infinium II Illumina BeadChips |
| snprma | Preprocessing tool for SNP arrays. |
| snprma2 | Preprocessing tool for SNP arrays. |
| snprmaAffy | Quantile normalize intensities for SNPs |
| tau2 | Accessors for batch-specific summary statistics. |
| tau2-method | Methods for class "AssayData" in crlmm |
| tau2-method | crlmm methods for class "CNSet" |
| totalCopynumber | Accessors for allele-specific or total copy number |
| totalCopynumber-method | crlmm methods for class "CNSet" |
| validCdfNames | Supported annotation packages for crlmm genotyping |
| validCEL | Reads cel files and return an error if a file is not read |
| xyplot | Plot prediction regions and normalized intensities. |
| xyplot-method | Plot prediction regions and normalized intensities. |
| [-method | Class '"PredictionRegion"' |